Emissions and Legal Issues
In most (if not all) cases, Honda Hybrids remain emissions legal, thanks to the low emissions levels of Honda engines. However to stay emissions legal, you will have to retain all the emissions hardware that came with the original chassis/engine or, even better, uprade the emissions hardware to the one that comes with the new motor.

The essential hardware that is required for legal emissions are:
catalytic converter of the correct type
properly functioning O2 sensor
properly function evaporative emissions hardware

Due to the different emissions testing standards in various states, a hybrid may not pass certain emissions requirements. For example, California vehicles have to pass a visual inspection in addition to the emissions tests.

Staying legal is not difficult too. Most states require that engines can only be replaced by engines of the same or later model-year vehicles. Hence, it is easier to find replacement engines for older cars than for newer cars. Some states keep a record of the engine serial numbers so make sure you update your vehicle registration with the new serial number.

One last thing. Make sure the engine has proper paperwork when you purchase it. Serial numbers are required to be on the engine, so that it is easily traceable. With the prices of certain engines skyrocketing due to the large demand, there is always a market for illegally acquired engines. I know of at least one HP list member who had his hybrid Prelude engine confisticated as it did not have a serial number.

Generation Specific Information
Detailed information specific to different models/generations and how each hybrid works out.

Honda Civic
3G Tech
4G Tech
5G Tech
6G Tech

Engine Wiring
So you've managed to shoehorn that engine in. What next? You'll have to wire it up of course! Use these wiring schema to make sure you have everything wired up correctly.

ECU Pinouts
B16A3 in EG Civic (92-95)
B18C1 in EG Civic (92-95)
Integra GSR wiring diagram
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ECU Pinouts
EG series Civic (5G, 92-95) and DC series Integra (3G, 94+)

OBD-II compliant ECU,
EK series Civic (6G, 96+) and DC series Integra (3G, 96+)

B16A3 in EG Civic

There are 6 lines to check on.

B18C1 in EG Civic

Check on the following 7 lines to see if everything is there and if they are hooked up right.